Hello MonUserCJ and welcome to the forum.
The simple answer to both of your questions is "Yes", most easily if you have Monarch Pro.
Based on your outline description there are likely to be a number of approaches possible, including the luxury of being able to tune the input reports to more accurately suit your needs - unusual for most situations.
It sounds like you may need to find an improved trapping method to ensure you get all the records you need to be extracting.
A common technique when the trqp picks up lines that are not required is to extract them into Monarch's table and then define a filter that does not select them for any further processing.
Being uncertain of the information you are thinking of as a footer I will be somewhat cautious about multi stage processing (you may not need the footer but I can't tell), but it is quiite usual to process several files (or one report fiel several ways) extracting specific information and exporting it to a common output structure record from each process. The export could be a database table or simply a fixed width column text file.
The extraction may be to separate files or tables or all into the same file or table. You can elect how to deal with it using a Project Export.
If you add everything to a single file/table you can then use that for the next analysis stage.
If you export to separate files/tables you may need to ensure you create a common 'key' file to bring them all back together again, especially if the different extracts are all parts of a 'master' record that need to be combined, eventually, into a single output analysis.
So that is the general response.
Usually something more specific to your requirements will be of greater help to you. The most effective approach for that is to post a representative sample of the report you are working with (modify any data that cannot be made public but at the same time don't destroy the 'flavour' of the output since that might be important for successful trapping and filtering. Representative TEST SYSTEM data is usually quite good.) There is a 'Sticky' post near the top of the forum that advises how best to post such information in order to retain the report format - important for designing traps and readability.